Study 2¶
Brief description of neuroimaging study.
Figure 2¶
Rather than selecting a few slices, let’s allow readers to interact with the entire statistical map!
import nibabel as nib
from nilearn.plotting import view_img
zmap = nib.load('data/unthresh_Z.nii.gz')
view_img(zmap, threshold=2.8)
Here is the statistic map on a surface mesh.
Supplemental Figure 3¶
from nilearn.plotting import view_img_on_surf
view_img_on_surf(zmap,threshold=2.8)
Table 2¶
We can also generate a coordinate table from the statistical map.
from nilearn.reporting import get_clusters_table
table = get_clusters_table(zmap,
stat_threshold=2.8,
cluster_threshold=10).set_index('Cluster ID',
drop=True)
display(table)
| X | Y | Z | Peak Stat | Cluster Size (mm3) | |
|---|---|---|---|---|---|
| Cluster ID | |||||
| 1 | -34.0 | 20.0 | 8.0 | 3.961450 | 832 |
| 2 | -40.0 | -54.0 | 50.0 | 3.916769 | 2800 |
| 2a | -34.0 | -64.0 | 38.0 | 3.624071 | |
| 2b | -36.0 | -56.0 | 40.0 | 3.511222 | |
| 2c | -46.0 | -42.0 | 44.0 | 3.082136 | |
| 3 | 10.0 | 36.0 | 22.0 | 3.871496 | 512 |
| 4 | -40.0 | 24.0 | 32.0 | 3.761007 | 1648 |
| 4a | -48.0 | 28.0 | 34.0 | 3.689187 | |
| 4b | -42.0 | 30.0 | 26.0 | 3.413833 | |
| 4c | -54.0 | 12.0 | 34.0 | 3.204023 | |
| 5 | 0.0 | 24.0 | 36.0 | 3.636167 | 3432 |
| 5a | -6.0 | 24.0 | 42.0 | 3.557699 | |
| 5b | -8.0 | 32.0 | 44.0 | 3.462496 | |
| 6 | -30.0 | 10.0 | 60.0 | 3.617460 | 272 |
| 6a | -30.0 | 2.0 | 64.0 | 3.185505 | |
| 7 | -38.0 | 44.0 | 0.0 | 3.396527 | 600 |
| 7a | -42.0 | 50.0 | 6.0 | 3.363012 | |
| 8 | -18.0 | 26.0 | 56.0 | 3.380708 | 240 |
| 9 | -10.0 | 38.0 | 18.0 | 3.372366 | 208 |
| 10 | 14.0 | 2.0 | -8.0 | 3.150095 | 80 |
| 11 | 42.0 | -56.0 | 52.0 | 3.104519 | 416 |
| 11a | 38.0 | -64.0 | 46.0 | 3.018312 |